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Merge branch 'master' into core-updates

master
Marius Bakke 2018-09-10 01:37:32 +02:00
parent fb94354a69 d4bd2453ec
commit fe79ce3b1f
No known key found for this signature in database
GPG Key ID: A2A06DF2A33A54FA
12 changed files with 299 additions and 32 deletions
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1
gnu/local.mk
View File

@ -721,6 +721,7 @@ dist_patch_DATA = \
%D%/packages/patches/gcr-disable-failing-tests.patch \
%D%/packages/patches/gcr-fix-collection-tests-to-work-with-gpg-21.patch \
%D%/packages/patches/gd-CVE-2018-5711.patch \
%D%/packages/patches/gd-CVE-2018-1000222.patch \
%D%/packages/patches/gd-fix-tests-on-i686.patch \
%D%/packages/patches/gd-freetype-test-failure.patch \
%D%/packages/patches/gdm-CVE-2018-14424.patch \

4
gnu/packages/bioconductor.scm
View File

@ -410,14 +410,14 @@ determining dependencies between variables, code improvement suggestions.")
(define-public r-chippeakanno
(package
(name "r-chippeakanno")
(version "3.14.1")
(version "3.14.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPpeakAnno" version))
(sha256
(base32
"1cn1hfc3nvsf2n3563lkmvwjxfbiygx7f84zk683p89gy7zi1gyj"))))
"13rksc65lxxzyw11galh6xzvgzp5ii0gwiwpvrm395v2r17rhwsc"))))
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs

4
gnu/packages/bioinformatics.scm
View File

@ -9866,14 +9866,14 @@ Shiny-based display methods for Bioconductor objects.")
(define-public r-annotationhub
(package
(name "r-annotationhub")
(version "2.12.0")
(version "2.12.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationHub" version))
(sha256
(base32
"11gh7qkgazs90czdqgv74gh2hz26xrmdp6wsz9x5pygbxls8xdw3"))))
"02ls279k1qlch147vw8kwvlhcqyzvi495bgv110m0xnnbpgbln6g"))))
(properties `((upstream-name . "AnnotationHub")))
(build-system r-build-system)
(propagated-inputs

11
gnu/packages/gd.scm
View File

@ -39,6 +39,7 @@
(define-public gd
(package
(name "gd")
(replacement gd/fixed)
;; Note: With libgd.org now pointing to github.com, genuine old
;; tarballs are no longer available. Notably, versions 2.0.x are
;; missing.
@ -91,6 +92,16 @@ most common applications of GD involve website development.")
"See COPYING file in the distribution."))
(properties '((cpe-name . "libgd")))))
(define-public gd/fixed
(hidden-package
(package
(inherit gd)
(source (origin
(inherit (package-source gd))
(patches (append (origin-patches (package-source gd))
(search-patches "gd-CVE-2018-5711.patch"
"gd-CVE-2018-1000222.patch"))))))))
(define-public perl-gd
(package
(name "perl-gd")

87
gnu/packages/patches/gd-CVE-2018-1000222.patch Normal file
View File

@ -0,0 +1,87 @@
Fix CVE-2018-1000222:
https://github.com/libgd/libgd/issues/447
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-1000222
Patch copied from upstream source repository:
https://github.com/libgd/libgd/commit/4b1e18a00ce7c4b7e6919c3b3109a034393b805a
From 4b1e18a00ce7c4b7e6919c3b3109a034393b805a Mon Sep 17 00:00:00 2001
From: Mike Frysinger <vapier@gentoo.org>
Date: Sat, 14 Jul 2018 13:54:08 -0400
Subject: [PATCH] bmp: check return value in gdImageBmpPtr
Closes #447.
(cherry picked from commit ac16bdf2d41724b5a65255d4c28fb0ec46bc42f5)
---
src/gd_bmp.c | 17 ++++++++++++++---
1 file changed, 14 insertions(+), 3 deletions(-)
diff --git a/src/gd_bmp.c b/src/gd_bmp.c
index ccafdcd..d625da1 100644
--- a/src/gd_bmp.c
+++ b/src/gd_bmp.c
@@ -48,6 +48,8 @@ static int bmp_read_4bit(gdImagePtr im, gdIOCtxPtr infile, bmp_info_t *info, bmp
static int bmp_read_8bit(gdImagePtr im, gdIOCtxPtr infile, bmp_info_t *info, bmp_hdr_t *header);
static int bmp_read_rle(gdImagePtr im, gdIOCtxPtr infile, bmp_info_t *info);
+static int _gdImageBmpCtx(gdImagePtr im, gdIOCtxPtr out, int compression);
+
#define BMP_DEBUG(s)
static int gdBMPPutWord(gdIOCtx *out, int w)
@@ -88,8 +90,10 @@ BGD_DECLARE(void *) gdImageBmpPtr(gdImagePtr im, int *size, int compression)
void *rv;
gdIOCtx *out = gdNewDynamicCtx(2048, NULL);
if (out == NULL) return NULL;
- gdImageBmpCtx(im, out, compression);
- rv = gdDPExtractData(out, size);
+ if (!_gdImageBmpCtx(im, out, compression))
+ rv = gdDPExtractData(out, size);
+ else
+ rv = NULL;
out->gd_free(out);
return rv;
}
@@ -142,6 +146,11 @@ BGD_DECLARE(void) gdImageBmp(gdImagePtr im, FILE *outFile, int compression)
compression - whether to apply RLE or not.
*/
BGD_DECLARE(void) gdImageBmpCtx(gdImagePtr im, gdIOCtxPtr out, int compression)
+{
+ _gdImageBmpCtx(im, out, compression);
+}
+
+static int _gdImageBmpCtx(gdImagePtr im, gdIOCtxPtr out, int compression)
{
int bitmap_size = 0, info_size, total_size, padding;
int i, row, xpos, pixel;
@@ -149,6 +158,7 @@ BGD_DECLARE(void) gdImageBmpCtx(gdImagePtr im, gdIOCtxPtr out, int compression)
unsigned char *uncompressed_row = NULL, *uncompressed_row_start = NULL;
FILE *tmpfile_for_compression = NULL;
gdIOCtxPtr out_original = NULL;
+ int ret = 1;
/* No compression if its true colour or we don't support seek */
if (im->trueColor) {
@@ -326,6 +336,7 @@ BGD_DECLARE(void) gdImageBmpCtx(gdImagePtr im, gdIOCtxPtr out, int compression)
out_original = NULL;
}
+ ret = 0;
cleanup:
if (tmpfile_for_compression) {
#ifdef _WIN32
@@ -339,7 +350,7 @@ cleanup:
if (out_original) {
out_original->gd_free(out_original);
}
- return;
+ return ret;
}
static int compress_row(unsigned char *row, int length)
--
2.18.0

3
gnu/packages/php.scm
View File

@ -57,7 +57,8 @@
(inherit (package-source gd))
(patches (search-patches "gd-fix-tests-on-i686.patch"
"gd-freetype-test-failure.patch"
"gd-CVE-2018-5711.patch"))))))
"gd-CVE-2018-5711.patch"
"gd-CVE-2018-1000222.patch"))))))
(define-public php
(package

4
gnu/packages/statistics.scm
View File

@ -1749,13 +1749,13 @@ and density estimation.")
(define-public r-chron
(package
(name "r-chron")
(version "2.3-52")
(version "2.3-53")
(source (origin
(method url-fetch)
(uri (cran-uri "chron" version))
(sha256
(base32
"185lfp75cv3l4cavg64sccj8lgc5sivch13n6gkannv3pd5cyzy4"))))
"02bkywwsxwrxc035hv51dxgdm1fjxdm7dn19ivifln59dfs1862j"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/chron")
(synopsis "Chronological R objects which can handle dates and times")

8
gnu/packages/tex.scm
View File

@ -4250,14 +4250,14 @@ PDF documents.")
(define-public texmaker
(package
(name "texmaker")
(version "4.5")
(version "5.0.2")
(source (origin
(method url-fetch)
(uri (string-append "http://www.xm1math.net/texmaker/texmaker-"
version ".tar.bz2"))
(sha256
(base32
"056njk6j8wma23mlp7xa3rgfaxx0q8ynwx8wkmj7iy0b85p9ds9c"))))
"0y81mjm89b99pr9svcwpaf4iz2q9pc9hjas5kiwd1pbgl5vqskm9"))))
(build-system gnu-build-system)
(arguments
`(#:phases
@ -4268,9 +4268,9 @@ PDF documents.")
(let ((out (assoc-ref outputs "out")))
(invoke "qmake"
(string-append "PREFIX=" out)
(string-append "DESKTOPDIR=" out
"/share/applications")
(string-append "DESKTOPDIR=" out "/share/applications")
(string-append "ICONDIR=" out "/share/pixmaps")
(string-append "METAINFODIR=" out "/share/metainfo")
"texmaker.pro")))))))
(inputs
`(("poppler-qt5" ,poppler-qt5)

8
gnu/packages/tls.scm
View File

@ -502,20 +502,20 @@ netcat implementation that supports TLS.")
(package
(name "python-acme")
;; Remember to update the hash of certbot when updating python-acme.
(version "0.26.1")
(version "0.27.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "acme" version))
(sha256
(base32
"1glhwqj6yyb11820lspgd0gl5dqdfljn43kcy4ar5caccpsbbrw6"))))
"142gynlfx7yv0sdba3gpdxlnhg9chhz7hpdxdrp630z17h1bk9ri"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'build 'build-documentation
(lambda _
(zero? (system* "make" "-C" "docs" "man" "info"))))
(invoke "make" "-C" "docs" "man" "info")))
(add-after 'install 'install-documentation
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
@ -559,7 +559,7 @@ netcat implementation that supports TLS.")
(uri (pypi-uri name version))
(sha256
(base32
"0rnayqhdabm0rljxh76blqd11h51dqnwlwvql0j6xwzpccym30s9"))))
"0anh3vjy9sif1bkp25nj76ii37xx8hh0igcx60ppag12xlabsw1m"))))
(build-system python-build-system)
(arguments
`(,@(substitute-keyword-arguments (package-arguments python-acme)

2
guix/scripts/build.scm
View File

@ -735,7 +735,7 @@ needed."
(parameterize ((current-build-output-port (if quiet?
(%make-void-port "w")
(current-error-port))))
(build-output-port #:verbose? #t))))
(let* ((mode (assoc-ref opts 'build-mode))
(drv (options->derivations store opts))
(urls (map (cut string-append <> "/log")

37
guix/scripts/package.scm
View File

@ -329,7 +329,8 @@ ENTRIES, a list of manifest entries, in the context of PROFILE."
`((verbosity . 0)
(graft? . #t)
(substitutes? . #t)
(build-hook? . #t)))
(build-hook? . #t)
(print-build-trace? . #t)))
(define (show-help)
(display (G_ "Usage: guix package [OPTION]...
@ -930,18 +931,24 @@ processed, #f otherwise."
(arg-handler arg result)
(leave (G_ "~A: extraneous argument~%") arg)))
(let ((opts (parse-command-line args %options (list %default-options #f)
#:argument-handler handle-argument)))
(with-error-handling
(or (process-query opts)
(parameterize ((%store (open-connection))
(%graft? (assoc-ref opts 'graft?)))
(set-build-options-from-command-line (%store) opts)
(define opts
(parse-command-line args %options (list %default-options #f)
#:argument-handler handle-argument))
(define verbose?
(assoc-ref opts 'verbose?))
(parameterize ((%guile-for-build
(package-derivation
(%store)
(if (assoc-ref opts 'bootstrap?)
%bootstrap-guile
(canonical-package guile-2.2)))))
(process-actions (%store) opts)))))))
(with-error-handling
(or (process-query opts)
(parameterize ((%store (open-connection))
(%graft? (assoc-ref opts 'graft?)))
(set-build-options-from-command-line (%store) opts)
(parameterize ((%guile-for-build
(package-derivation
(%store)
(if (assoc-ref opts 'bootstrap?)
%bootstrap-guile
(canonical-package guile-2.2))))
(current-build-output-port
(build-output-port #:verbose? verbose?)))
(process-actions (%store) opts))))))

162
guix/ui.scm
View File

@ -10,6 +10,9 @@
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016 Benz Schenk <benz.schenk@uzh.ch>
;;; Copyright © 2018 Kyle Meyer <kyle@kyleam.com>
;;; Copyright © 2013, 2014 Free Software Foundation, Inc.
;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; This file is part of GNU Guix.
;;;
@ -115,7 +118,8 @@
guix-warning-port
warning
info
guix-main))
guix-main
build-output-port))
;;; Commentary:
;;;
@ -1622,4 +1626,160 @@ and signal handling has already been set up."
(initialize-guix)
(apply run-guix args))
(define color-table
`((CLEAR . "0")
(RESET . "0")
(BOLD . "1")
(DARK . "2")
(UNDERLINE . "4")
(UNDERSCORE . "4")
(BLINK . "5")
(REVERSE . "6")
(CONCEALED . "8")
(BLACK . "30")
(RED . "31")
(GREEN . "32")
(YELLOW . "33")
(BLUE . "34")
(MAGENTA . "35")
(CYAN . "36")
(WHITE . "37")
(ON-BLACK . "40")
(ON-RED . "41")
(ON-GREEN . "42")
(ON-YELLOW . "43")
(ON-BLUE . "44")
(ON-MAGENTA . "45")
(ON-CYAN . "46")
(ON-WHITE . "47")))
(define (color . lst)
"Return a string containing the ANSI escape sequence for producing the
requested set of attributes in LST. Unknown attributes are ignored."
(let ((color-list
(remove not
(map (lambda (color) (assq-ref color-table color))
lst))))
(if (null? color-list)
""
(string-append
(string #\esc #\[)
(string-join color-list ";" 'infix)
"m"))))
(define (colorize-string str . color-list)
"Return a copy of STR colorized using ANSI escape sequences according to the
attributes STR. At the end of the returned string, the color attributes will
be reset such that subsequent output will not have any colors in effect."
(string-append
(apply color color-list)
str
(color 'RESET)))
(define* (build-output-port #:key
(colorize? #t)
verbose?
(port (current-error-port)))
"Return a soft port that processes build output. By default it colorizes
phase announcements and replaces any other output with a spinner."
(define spun? #f)
(define spin!
(let ((steps (circular-list "\\" "|" "/" "-")))
(lambda ()
(match steps
((first . rest)
(set! steps rest)
(set! spun? #t) ; remember to erase spinner
first)))))
(define use-color?
(and colorize?
(not (or (getenv "NO_COLOR")
(getenv "INSIDE_EMACS")
(not (isatty? port))))))
(define handle-string
(let* ((proc (if use-color?
colorize-string
(lambda (s . _) s)))
(rules `(("^(@ build-started) (.*) (.*)"
#:transform
,(lambda (m)
(string-append
(proc "Building " 'BLUE 'BOLD)
(match:substring m 2) "\n")))
("^(@ build-failed) (.*) (.*)"
#:transform
,(lambda (m)
(string-append
(proc "Build failed: " 'RED 'BOLD)
(match:substring m 2) "\n")))
("^(@ build-succeeded) (.*) (.*)"
#:transform
,(lambda (m)
(string-append
(proc "Built " 'GREEN 'BOLD)
(match:substring m 2) "\n")))
("^(@ substituter-started) (.*) (.*)"
#:transform
,(lambda (m)
(string-append
(proc "Substituting " 'BLUE 'BOLD)
(match:substring m 2) "\n")))
("^(@ substituter-failed) (.*) (.*) (.*)"
#:transform
,(lambda (m)
(string-append
(proc "Substituter failed: " 'RED 'BOLD)
(match:substring m 2) "\n"
(match:substring m 3) ": "
(match:substring m 4) "\n")))
("^(@ substituter-succeeded) (.*)"
#:transform
,(lambda (m)
(string-append
(proc "Substituted " 'GREEN 'BOLD)
(match:substring m 2) "\n")))
("^(starting phase )(.*)"
BLUE GREEN)
("^(phase)(.*)(succeeded after)(.*)(seconds)(.*)"
GREEN BLUE GREEN BLUE GREEN BLUE)
("^(phase)(.*)(failed after)(.*)(seconds)(.*)"
RED BLUE RED BLUE RED BLUE))))
(lambda (str)
(let ((processed
(any (match-lambda
((pattern #:transform transform)
(and=> (string-match pattern str)
transform))
((pattern . colors)
(and=> (string-match pattern str)
(lambda (m)
(let ((substrings
(map (cut match:substring m <>)
(iota (- (match:count m) 1) 1))))
(string-join (map proc substrings colors) ""))))))
rules)))
(when spun?
(display (string #\backspace) port))
(if processed
(begin
(display processed port)
(set! spun? #f))
;; Print unprocessed line, or replace with spinner
(display (if verbose? str (spin!)) port))))))
(make-soft-port
(vector
;; procedure accepting one character for output
(cut write <> port)
;; procedure accepting a string for output
handle-string
;; thunk for flushing output
(lambda () (force-output port))
;; thunk for getting one character
(const #t)
;; thunk for closing port (not by garbage collection)
(lambda () (close port)))
"w"))
;;; ui.scm ends here